Entering edit mode
4.3 years ago
lucie.semenec
•
0
Hello,
I have used clusterProfiler to get Kegg entry names from uniprot IDs:
keggID<-bitr_kegg(uniID, fromType='uniprot', toType='kegg', organism='abau') which gives the resulting dataframe:
> str(keggID)
'data.frame': 1055 obs. of 2 variables:
$ uniprot: chr "A0A059ZNF8" "A0A0D8E944" "V5VFS9" "V5VH39" ...
$ kegg : chr "IX87_00060" "IX87_00090" "IX87_00345" "IX87_00350" ...
and where uniID looks like:
> str(uniID)
chr [1:3862] "A0A059ZTB3" "V5V7W3" "A0A0C0B3P7" "A0A0D5YCW0" "A0A059ZT40" "V5V8D0" "A0A0D5YC24" "A0A059ZJ30"
However, I would like to use the reconstruct pathway tool in KEGG mapper (https://www.kegg.jp/kegg/tool/map_pathway.html) but it requires a gene list KO annotation file where each gene has a corresponding K number instead of kegg entry name. For example:
gene1 K02874
gene4 K00416
gene7 K12864
gene10 K03695
Is there any way to get the "K" numbers from the Kegg entry names bitr_kegg() function gave me (ie. IX87_00060) or from uniprot names?
Thanks very much in advance!